1 Data preparation

1.1 Outline

  • Load scripts: loads libraries and useful scripts used in the analyses; all .R files contained in scripts at the root of the factory are automatically loaded

  • Load data: imports datasets, and may contain some ad hoc changes to the data such as specific data cleaning (not used in other reports), new variables used in the analyses, etc.

1.2 Load packages


library(reportfactory)
library(here)
library(rio) 
library(tidyverse)
library(incidence)
library(distcrete)
library(epitrix)
library(earlyR)
library(projections)
library(linelist)
library(remotes)
library(janitor)
library(kableExtra)
library(DT)
library(cyphr)
library(chngpt)
library(lubridate)
library(ggpubr)
library(ggnewscale)

1.3 Load scripts

These scripts will load:

  • all scripts stored as .R files inside /scripts/
  • all scripts stored as .R files inside /src/

These scripts also contain routines to access the latest clean encrypted data (see next section).


reportfactory::rfh_load_scripts()

1.4 Load clean data

We import the latest NHS pathways data:


x <- import_pathways() %>%
  as_tibble()
x
## # A tibble: 332,324 x 11
##    site_type date       sex   age   ccg_code ccg_name count postcode nhs_region
##    <chr>     <date>     <chr> <chr> <chr>    <chr>    <int> <chr>    <chr>     
##  1 111       2020-03-18 fema… miss… e380000… nhs_glo…     1 gl34fe   South West
##  2 111       2020-03-18 fema… miss… e380001… nhs_sou…     1 ne325nn  North Eas…
##  3 111       2020-03-18 fema… 0-18  e380000… nhs_air…     8 bd57jr   North Eas…
##  4 111       2020-03-18 fema… 0-18  e380000… nhs_ash…     7 tn254ab  South East
##  5 111       2020-03-18 fema… 0-18  e380000… nhs_bar…    35 rm13ae   London    
##  6 111       2020-03-18 fema… 0-18  e380000… nhs_bar…     9 n111np   London    
##  7 111       2020-03-18 fema… 0-18  e380000… nhs_bar…    11 s752py   North Eas…
##  8 111       2020-03-18 fema… 0-18  e380000… nhs_bas…    19 ss143hg  East of E…
##  9 111       2020-03-18 fema… 0-18  e380000… nhs_bas…     6 dn227xf  North Eas…
## 10 111       2020-03-18 fema… 0-18  e380000… nhs_bat…     9 ba25rp   South West
## # … with 332,314 more rows, and 2 more variables: day <int>, weekday <fct>

We also import demographics data for NHS regions in England, used later in our analysis:


path <- here::here("data", "csv", "nhs_region_population_2018.csv")
nhs_region_pop <- rio::import(path) %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

nhs_region_pop$nhs_region <- gsub(" Of ", " of ", nhs_region_pop$nhs_region)
nhs_region_pop$nhs_region <- gsub(" And ", " and ", nhs_region_pop$nhs_region)
nhs_region_pop
##                  nhs_region variable      value
## 1                North West     0-18 0.22538599
## 2  North East and Yorkshire     0-18 0.21876449
## 3                  Midlands     0-18 0.22564656
## 4           East of England     0-18 0.22810783
## 5                    London     0-18 0.23764782
## 6                South East     0-18 0.22458811
## 7                South West     0-18 0.20799797
## 8                North West    19-69 0.64274078
## 9  North East and Yorkshire    19-69 0.64437753
## 10                 Midlands    19-69 0.63876675
## 11          East of England    19-69 0.63034229
## 12                   London    19-69 0.67820084
## 13               South East    19-69 0.63267336
## 14               South West    19-69 0.63176131
## 15               North West   70-120 0.13187323
## 16 North East and Yorkshire   70-120 0.13685797
## 17                 Midlands   70-120 0.13558669
## 18          East of England   70-120 0.14154988
## 19                   London   70-120 0.08415135
## 20               South East   70-120 0.14273853
## 21               South West   70-120 0.16024072

Finally, we import publically available deaths per NHS region:


dth <- import_deaths() %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

#truncation to account for reporting delay
delay_max <- 21

dth$nhs_region <- gsub(" Of ", " of ", dth$nhs_region)
dth$nhs_region <- gsub(" And ", " and ", dth$nhs_region)
dth
##      date_report               nhs_region deaths
## 1     2020-03-01          East of England      0
## 2     2020-03-02          East of England      1
## 3     2020-03-03          East of England      0
## 4     2020-03-04          East of England      0
## 5     2020-03-05          East of England      0
## 6     2020-03-06          East of England      1
## 7     2020-03-07          East of England      0
## 8     2020-03-08          East of England      0
## 9     2020-03-09          East of England      1
## 10    2020-03-10          East of England      0
## 11    2020-03-11          East of England      0
## 12    2020-03-12          East of England      0
## 13    2020-03-13          East of England      1
## 14    2020-03-14          East of England      2
## 15    2020-03-15          East of England      2
## 16    2020-03-16          East of England      1
## 17    2020-03-17          East of England      1
## 18    2020-03-18          East of England      5
## 19    2020-03-19          East of England      4
## 20    2020-03-20          East of England      2
## 21    2020-03-21          East of England     11
## 22    2020-03-22          East of England     12
## 23    2020-03-23          East of England     11
## 24    2020-03-24          East of England     19
## 25    2020-03-25          East of England     26
## 26    2020-03-26          East of England     36
## 27    2020-03-27          East of England     38
## 28    2020-03-28          East of England     28
## 29    2020-03-29          East of England     43
## 30    2020-03-30          East of England     45
## 31    2020-03-31          East of England     70
## 32    2020-04-01          East of England     62
## 33    2020-04-02          East of England     65
## 34    2020-04-03          East of England     80
## 35    2020-04-04          East of England     71
## 36    2020-04-05          East of England     76
## 37    2020-04-06          East of England     71
## 38    2020-04-07          East of England     93
## 39    2020-04-08          East of England    111
## 40    2020-04-09          East of England     87
## 41    2020-04-10          East of England     74
## 42    2020-04-11          East of England     92
## 43    2020-04-12          East of England    100
## 44    2020-04-13          East of England     78
## 45    2020-04-14          East of England     61
## 46    2020-04-15          East of England     82
## 47    2020-04-16          East of England     74
## 48    2020-04-17          East of England     86
## 49    2020-04-18          East of England     64
## 50    2020-04-19          East of England     67
## 51    2020-04-20          East of England     67
## 52    2020-04-21          East of England     75
## 53    2020-04-22          East of England     67
## 54    2020-04-23          East of England     49
## 55    2020-04-24          East of England     66
## 56    2020-04-25          East of England     54
## 57    2020-04-26          East of England     48
## 58    2020-04-27          East of England     46
## 59    2020-04-28          East of England     58
## 60    2020-04-29          East of England     32
## 61    2020-04-30          East of England     45
## 62    2020-05-01          East of England     49
## 63    2020-05-02          East of England     29
## 64    2020-05-03          East of England     41
## 65    2020-05-04          East of England     19
## 66    2020-05-05          East of England     36
## 67    2020-05-06          East of England     31
## 68    2020-05-07          East of England     33
## 69    2020-05-08          East of England     33
## 70    2020-05-09          East of England     29
## 71    2020-05-10          East of England     22
## 72    2020-05-11          East of England     18
## 73    2020-05-12          East of England     21
## 74    2020-05-13          East of England     27
## 75    2020-05-14          East of England     26
## 76    2020-05-15          East of England     19
## 77    2020-05-16          East of England     26
## 78    2020-05-17          East of England     17
## 79    2020-05-18          East of England     25
## 80    2020-05-19          East of England     15
## 81    2020-05-20          East of England     26
## 82    2020-05-21          East of England     21
## 83    2020-05-22          East of England     13
## 84    2020-05-23          East of England     12
## 85    2020-05-24          East of England     17
## 86    2020-05-25          East of England     25
## 87    2020-05-26          East of England     14
## 88    2020-05-27          East of England     12
## 89    2020-05-28          East of England     17
## 90    2020-05-29          East of England     16
## 91    2020-05-30          East of England      9
## 92    2020-05-31          East of England      8
## 93    2020-06-01          East of England     17
## 94    2020-06-02          East of England     14
## 95    2020-06-03          East of England     10
## 96    2020-06-04          East of England      7
## 97    2020-06-05          East of England     14
## 98    2020-06-06          East of England      5
## 99    2020-06-07          East of England      9
## 100   2020-06-08          East of England      7
## 101   2020-06-09          East of England      6
## 102   2020-06-10          East of England      8
## 103   2020-06-11          East of England      1
## 104   2020-06-12          East of England      9
## 105   2020-06-13          East of England      5
## 106   2020-06-14          East of England      4
## 107   2020-06-15          East of England      8
## 108   2020-06-16          East of England      3
## 109   2020-06-17          East of England      7
## 110   2020-06-18          East of England      4
## 111   2020-06-19          East of England      7
## 112   2020-06-20          East of England      4
## 113   2020-06-21          East of England      3
## 114   2020-06-22          East of England      6
## 115   2020-06-23          East of England      5
## 116   2020-06-24          East of England      4
## 117   2020-06-25          East of England      1
## 118   2020-06-26          East of England      5
## 119   2020-06-27          East of England      6
## 120   2020-06-28          East of England      8
## 121   2020-06-29          East of England      4
## 122   2020-06-30          East of England      5
## 123   2020-07-01          East of England      2
## 124   2020-07-02          East of England      5
## 125   2020-07-03          East of England      0
## 126   2020-07-04          East of England      3
## 127   2020-07-05          East of England      1
## 128   2020-07-06          East of England      2
## 129   2020-07-07          East of England      2
## 130   2020-07-08          East of England      0
## 131   2020-07-09          East of England      8
## 132   2020-07-10          East of England      4
## 133   2020-07-11          East of England      2
## 134   2020-07-12          East of England      1
## 135   2020-07-13          East of England      8
## 136   2020-07-14          East of England      2
## 137   2020-07-15          East of England      0
## 138   2020-07-16          East of England      0
## 139   2020-07-17          East of England      0
## 140   2020-07-18          East of England      0
## 141   2020-07-19          East of England      1
## 142   2020-07-20          East of England      1
## 143   2020-07-21          East of England      1
## 144   2020-07-22          East of England      2
## 145   2020-07-23          East of England      1
## 146   2020-07-24          East of England      1
## 147   2020-07-25          East of England      0
## 148   2020-07-26          East of England      1
## 149   2020-07-27          East of England      1
## 150   2020-07-28          East of England      2
## 151   2020-07-29          East of England      0
## 152   2020-07-30          East of England      0
## 153   2020-07-31          East of England      1
## 154   2020-08-01          East of England      0
## 155   2020-08-02          East of England      0
## 156   2020-08-03          East of England      0
## 157   2020-08-04          East of England      1
## 158   2020-08-05          East of England      1
## 159   2020-08-06          East of England      0
## 160   2020-08-07          East of England      1
## 161   2020-08-08          East of England      0
## 162   2020-08-09          East of England      0
## 163   2020-08-10          East of England      1
## 164   2020-08-11          East of England      2
## 165   2020-08-12          East of England      1
## 166   2020-08-13          East of England      0
## 167   2020-08-14          East of England      1
## 168   2020-08-15          East of England      1
## 169   2020-08-16          East of England      0
## 170   2020-08-17          East of England      0
## 171   2020-08-18          East of England      2
## 172   2020-08-19          East of England      1
## 173   2020-08-20          East of England      1
## 174   2020-08-21          East of England      0
## 175   2020-08-22          East of England      1
## 176   2020-08-23          East of England      1
## 177   2020-08-24          East of England      0
## 178   2020-08-25          East of England      0
## 179   2020-08-26          East of England      1
## 180   2020-08-27          East of England      1
## 181   2020-08-28          East of England      0
## 182   2020-08-29          East of England      0
## 183   2020-08-30          East of England      0
## 184   2020-08-31          East of England      0
## 185   2020-09-01          East of England      0
## 186   2020-09-02          East of England      0
## 187   2020-09-03          East of England      1
## 188   2020-09-04          East of England      1
## 189   2020-09-05          East of England      0
## 190   2020-09-06          East of England      1
## 191   2020-09-07          East of England      0
## 192   2020-09-08          East of England      0
## 193   2020-09-09          East of England      0
## 194   2020-09-10          East of England      0
## 195   2020-09-11          East of England      0
## 196   2020-09-12          East of England      0
## 197   2020-09-13          East of England      1
## 198   2020-09-14          East of England      1
## 199   2020-09-15          East of England      0
## 200   2020-09-16          East of England      0
## 201   2020-09-17          East of England      0
## 202   2020-09-18          East of England      0
## 203   2020-09-19          East of England      0
## 204   2020-09-20          East of England      2
## 205   2020-09-21          East of England      0
## 206   2020-09-22          East of England      2
## 207   2020-09-23          East of England      1
## 208   2020-09-24          East of England      0
## 209   2020-09-25          East of England      1
## 210   2020-09-26          East of England      1
## 211   2020-09-27          East of England      1
## 212   2020-09-28          East of England      2
## 213   2020-09-29          East of England      2
## 214   2020-09-30          East of England      2
## 215   2020-10-01          East of England      2
## 216   2020-10-02          East of England      1
## 217   2020-10-03          East of England      1
## 218   2020-10-04          East of England      0
## 219   2020-10-05          East of England      0
## 220   2020-10-06          East of England      4
## 221   2020-10-07          East of England      6
## 222   2020-10-08          East of England      3
## 223   2020-10-09          East of England      1
## 224   2020-10-10          East of England      6
## 225   2020-10-11          East of England      2
## 226   2020-10-12          East of England      2
## 227   2020-10-13          East of England      1
## 228   2020-10-14          East of England      3
## 229   2020-10-15          East of England      4
## 230   2020-10-16          East of England      5
## 231   2020-10-17          East of England      6
## 232   2020-10-18          East of England      7
## 233   2020-10-19          East of England      5
## 234   2020-10-20          East of England      9
## 235   2020-10-21          East of England      7
## 236   2020-10-22          East of England      7
## 237   2020-10-23          East of England     14
## 238   2020-10-24          East of England      1
## 239   2020-10-25          East of England     10
## 240   2020-10-26          East of England     10
## 241   2020-10-27          East of England      6
## 242   2020-10-28          East of England     12
## 243   2020-10-29          East of England     10
## 244   2020-10-30          East of England     12
## 245   2020-10-31          East of England     15
## 246   2020-11-01          East of England     14
## 247   2020-11-02          East of England      8
## 248   2020-11-03          East of England     14
## 249   2020-11-04          East of England     10
## 250   2020-11-05          East of England     10
## 251   2020-11-06          East of England     17
## 252   2020-11-07          East of England     10
## 253   2020-11-08          East of England     13
## 254   2020-11-09          East of England     13
## 255   2020-11-10          East of England     26
## 256   2020-11-11          East of England     14
## 257   2020-11-12          East of England     13
## 258   2020-11-13          East of England     21
## 259   2020-11-14          East of England     18
## 260   2020-11-15          East of England     13
## 261   2020-11-16          East of England     11
## 262   2020-11-17          East of England     16
## 263   2020-11-18          East of England     16
## 264   2020-11-19          East of England      3
## 265   2020-03-01                   London      0
## 266   2020-03-02                   London      0
## 267   2020-03-03                   London      0
## 268   2020-03-04                   London      0
## 269   2020-03-05                   London      0
## 270   2020-03-06                   London      1
## 271   2020-03-07                   London      0
## 272   2020-03-08                   London      0
## 273   2020-03-09                   London      1
## 274   2020-03-10                   London      0
## 275   2020-03-11                   London      5
## 276   2020-03-12                   London      6
## 277   2020-03-13                   London     10
## 278   2020-03-14                   London     13
## 279   2020-03-15                   London      9
## 280   2020-03-16                   London     15
## 281   2020-03-17                   London     23
## 282   2020-03-18                   London     28
## 283   2020-03-19                   London     25
## 284   2020-03-20                   London     44
## 285   2020-03-21                   London     49
## 286   2020-03-22                   London     54
## 287   2020-03-23                   London     63
## 288   2020-03-24                   London     86
## 289   2020-03-25                   London    112
## 290   2020-03-26                   London    129
## 291   2020-03-27                   London    130
## 292   2020-03-28                   London    123
## 293   2020-03-29                   London    145
## 294   2020-03-30                   London    151
## 295   2020-03-31                   London    183
## 296   2020-04-01                   London    202
## 297   2020-04-02                   London    191
## 298   2020-04-03                   London    199
## 299   2020-04-04                   London    231
## 300   2020-04-05                   London    195
## 301   2020-04-06                   London    198
## 302   2020-04-07                   London    220
## 303   2020-04-08                   London    239
## 304   2020-04-09                   London    207
## 305   2020-04-10                   London    171
## 306   2020-04-11                   London    178
## 307   2020-04-12                   London    158
## 308   2020-04-13                   London    166
## 309   2020-04-14                   London    143
## 310   2020-04-15                   London    143
## 311   2020-04-16                   London    140
## 312   2020-04-17                   London    101
## 313   2020-04-18                   London    101
## 314   2020-04-19                   London    103
## 315   2020-04-20                   London     96
## 316   2020-04-21                   London     96
## 317   2020-04-22                   London    109
## 318   2020-04-23                   London     77
## 319   2020-04-24                   London     71
## 320   2020-04-25                   London     58
## 321   2020-04-26                   London     53
## 322   2020-04-27                   London     52
## 323   2020-04-28                   London     44
## 324   2020-04-29                   London     45
## 325   2020-04-30                   London     40
## 326   2020-05-01                   London     41
## 327   2020-05-02                   London     41
## 328   2020-05-03                   London     36
## 329   2020-05-04                   London     30
## 330   2020-05-05                   London     25
## 331   2020-05-06                   London     37
## 332   2020-05-07                   London     37
## 333   2020-05-08                   London     30
## 334   2020-05-09                   London     23
## 335   2020-05-10                   London     26
## 336   2020-05-11                   London     18
## 337   2020-05-12                   London     18
## 338   2020-05-13                   London     17
## 339   2020-05-14                   London     20
## 340   2020-05-15                   London     19
## 341   2020-05-16                   London     14
## 342   2020-05-17                   London     15
## 343   2020-05-18                   London     11
## 344   2020-05-19                   London     14
## 345   2020-05-20                   London     19
## 346   2020-05-21                   London     12
## 347   2020-05-22                   London     10
## 348   2020-05-23                   London      6
## 349   2020-05-24                   London      7
## 350   2020-05-25                   London      9
## 351   2020-05-26                   London     14
## 352   2020-05-27                   London      7
## 353   2020-05-28                   London      8
## 354   2020-05-29                   London      7
## 355   2020-05-30                   London     12
## 356   2020-05-31                   London      6
## 357   2020-06-01                   London     10
## 358   2020-06-02                   London      8
## 359   2020-06-03                   London      6
## 360   2020-06-04                   London      8
## 361   2020-06-05                   London      4
## 362   2020-06-06                   London      0
## 363   2020-06-07                   London      5
## 364   2020-06-08                   London      5
## 365   2020-06-09                   London      5
## 366   2020-06-10                   London      8
## 367   2020-06-11                   London      5
## 368   2020-06-12                   London      3
## 369   2020-06-13                   London      3
## 370   2020-06-14                   London      3
## 371   2020-06-15                   London      1
## 372   2020-06-16                   London      2
## 373   2020-06-17                   London      1
## 374   2020-06-18                   London      2
## 375   2020-06-19                   London      5
## 376   2020-06-20                   London      3
## 377   2020-06-21                   London      4
## 378   2020-06-22                   London      2
## 379   2020-06-23                   London      1
## 380   2020-06-24                   London      4
## 381   2020-06-25                   London      3
## 382   2020-06-26                   London      2
## 383   2020-06-27                   London      1
## 384   2020-06-28                   London      2
## 385   2020-06-29                   London      2
## 386   2020-06-30                   London      1
## 387   2020-07-01                   London      3
## 388   2020-07-02                   London      2
## 389   2020-07-03                   London      2
## 390   2020-07-04                   London      1
## 391   2020-07-05                   London      3
## 392   2020-07-06                   London      2
## 393   2020-07-07                   London      1
## 394   2020-07-08                   London      3
## 395   2020-07-09                   London      4
## 396   2020-07-10                   London      0
## 397   2020-07-11                   London      1
## 398   2020-07-12                   London      1
## 399   2020-07-13                   London      1
## 400   2020-07-14                   London      0
## 401   2020-07-15                   London      2
## 402   2020-07-16                   London      0
## 403   2020-07-17                   London      0
## 404   2020-07-18                   London      2
## 405   2020-07-19                   London      0
## 406   2020-07-20                   London      0
## 407   2020-07-21                   London      1
## 408   2020-07-22                   London      0
## 409   2020-07-23                   London      2
## 410   2020-07-24                   London      0
## 411   2020-07-25                   London      1
## 412   2020-07-26                   London      0
## 413   2020-07-27                   London      1
## 414   2020-07-28                   London      0
## 415   2020-07-29                   London      0
## 416   2020-07-30                   London      1
## 417   2020-07-31                   London      0
## 418   2020-08-01                   London      0
## 419   2020-08-02                   London      3
## 420   2020-08-03                   London      0
## 421   2020-08-04                   London      0
## 422   2020-08-05                   London      0
## 423   2020-08-06                   London      1
## 424   2020-08-07                   London      0
## 425   2020-08-08                   London      0
## 426   2020-08-09                   London      0
## 427   2020-08-10                   London      0
## 428   2020-08-11                   London      1
## 429   2020-08-12                   London      0
## 430   2020-08-13                   London      2
## 431   2020-08-14                   London      0
## 432   2020-08-15                   London      0
## 433   2020-08-16                   London      0
## 434   2020-08-17                   London      1
## 435   2020-08-18                   London      1
## 436   2020-08-19                   London      0
## 437   2020-08-20                   London      1
## 438   2020-08-21                   London      0
## 439   2020-08-22                   London      0
## 440   2020-08-23                   London      0
## 441   2020-08-24                   London      1
## 442   2020-08-25                   London      1
## 443   2020-08-26                   London      0
## 444   2020-08-27                   London      0
## 445   2020-08-28                   London      0
## 446   2020-08-29                   London      0
## 447   2020-08-30                   London      0
## 448   2020-08-31                   London      1
## 449   2020-09-01                   London      0
## 450   2020-09-02                   London      1
## 451   2020-09-03                   London      1
## 452   2020-09-04                   London      0
## 453   2020-09-05                   London      0
## 454   2020-09-06                   London      2
## 455   2020-09-07                   London      0
## 456   2020-09-08                   London      0
## 457   2020-09-09                   London      0
## 458   2020-09-10                   London      2
## 459   2020-09-11                   London      1
## 460   2020-09-12                   London      1
## 461   2020-09-13                   London      0
## 462   2020-09-14                   London      0
## 463   2020-09-15                   London      1
## 464   2020-09-16                   London      2
## 465   2020-09-17                   London      2
## 466   2020-09-18                   London      1
## 467   2020-09-19                   London      3
## 468   2020-09-20                   London      3
## 469   2020-09-21                   London      2
## 470   2020-09-22                   London      6
## 471   2020-09-23                   London      4
## 472   2020-09-24                   London      3
## 473   2020-09-25                   London      1
## 474   2020-09-26                   London      1
## 475   2020-09-27                   London      1
## 476   2020-09-28                   London      3
## 477   2020-09-29                   London      7
## 478   2020-09-30                   London      6
## 479   2020-10-01                   London      4
## 480   2020-10-02                   London      1
## 481   2020-10-03                   London      3
## 482   2020-10-04                   London      2
## 483   2020-10-05                   London      7
## 484   2020-10-06                   London      4
## 485   2020-10-07                   London      6
## 486   2020-10-08                   London      6
## 487   2020-10-09                   London      7
## 488   2020-10-10                   London      3
## 489   2020-10-11                   London      5
## 490   2020-10-12                   London      7
## 491   2020-10-13                   London      4
## 492   2020-10-14                   London      5
## 493   2020-10-15                   London     13
## 494   2020-10-16                   London      6
## 495   2020-10-17                   London      2
## 496   2020-10-18                   London      5
## 497   2020-10-19                   London     11
## 498   2020-10-20                   London      8
## 499   2020-10-21                   London     14
## 500   2020-10-22                   London     12
## 501   2020-10-23                   London      7
## 502   2020-10-24                   London     18
## 503   2020-10-25                   London     10
## 504   2020-10-26                   London     10
## 505   2020-10-27                   London     12
## 506   2020-10-28                   London     22
## 507   2020-10-29                   London     14
## 508   2020-10-30                   London     17
## 509   2020-10-31                   London      7
## 510   2020-11-01                   London     16
## 511   2020-11-02                   London     15
## 512   2020-11-03                   London     10
## 513   2020-11-04                   London     17
## 514   2020-11-05                   London     17
## 515   2020-11-06                   London     12
## 516   2020-11-07                   London     20
## 517   2020-11-08                   London     12
## 518   2020-11-09                   London     25
## 519   2020-11-10                   London     14
## 520   2020-11-11                   London     14
## 521   2020-11-12                   London     13
## 522   2020-11-13                   London     12
## 523   2020-11-14                   London     20
## 524   2020-11-15                   London     16
## 525   2020-11-16                   London     23
## 526   2020-11-17                   London     25
## 527   2020-11-18                   London     13
## 528   2020-11-19                   London      4
## 529   2020-03-01                 Midlands      0
## 530   2020-03-02                 Midlands      0
## 531   2020-03-03                 Midlands      1
## 532   2020-03-04                 Midlands      0
## 533   2020-03-05                 Midlands      0
## 534   2020-03-06                 Midlands      0
## 535   2020-03-07                 Midlands      0
## 536   2020-03-08                 Midlands      2
## 537   2020-03-09                 Midlands      1
## 538   2020-03-10                 Midlands      0
## 539   2020-03-11                 Midlands      2
## 540   2020-03-12                 Midlands      6
## 541   2020-03-13                 Midlands      5
## 542   2020-03-14                 Midlands      4
## 543   2020-03-15                 Midlands      5
## 544   2020-03-16                 Midlands     11
## 545   2020-03-17                 Midlands      8
## 546   2020-03-18                 Midlands     13
## 547   2020-03-19                 Midlands      8
## 548   2020-03-20                 Midlands     28
## 549   2020-03-21                 Midlands     13
## 550   2020-03-22                 Midlands     31
## 551   2020-03-23                 Midlands     33
## 552   2020-03-24                 Midlands     41
## 553   2020-03-25                 Midlands     48
## 554   2020-03-26                 Midlands     64
## 555   2020-03-27                 Midlands     72
## 556   2020-03-28                 Midlands     89
## 557   2020-03-29                 Midlands     92
## 558   2020-03-30                 Midlands     90
## 559   2020-03-31                 Midlands    123
## 560   2020-04-01                 Midlands    140
## 561   2020-04-02                 Midlands    142
## 562   2020-04-03                 Midlands    124
## 563   2020-04-04                 Midlands    151
## 564   2020-04-05                 Midlands    164
## 565   2020-04-06                 Midlands    140
## 566   2020-04-07                 Midlands    123
## 567   2020-04-08                 Midlands    186
## 568   2020-04-09                 Midlands    139
## 569   2020-04-10                 Midlands    127
## 570   2020-04-11                 Midlands    142
## 571   2020-04-12                 Midlands    139
## 572   2020-04-13                 Midlands    120
## 573   2020-04-14                 Midlands    116
## 574   2020-04-15                 Midlands    147
## 575   2020-04-16                 Midlands    102
## 576   2020-04-17                 Midlands    118
## 577   2020-04-18                 Midlands    115
## 578   2020-04-19                 Midlands     92
## 579   2020-04-20                 Midlands    107
## 580   2020-04-21                 Midlands     86
## 581   2020-04-22                 Midlands     78
## 582   2020-04-23                 Midlands    103
## 583   2020-04-24                 Midlands     79
## 584   2020-04-25                 Midlands     72
## 585   2020-04-26                 Midlands     81
## 586   2020-04-27                 Midlands     74
## 587   2020-04-28                 Midlands     68
## 588   2020-04-29                 Midlands     53
## 589   2020-04-30                 Midlands     56
## 590   2020-05-01                 Midlands     64
## 591   2020-05-02                 Midlands     51
## 592   2020-05-03                 Midlands     52
## 593   2020-05-04                 Midlands     61
## 594   2020-05-05                 Midlands     59
## 595   2020-05-06                 Midlands     59
## 596   2020-05-07                 Midlands     48
## 597   2020-05-08                 Midlands     34
## 598   2020-05-09                 Midlands     37
## 599   2020-05-10                 Midlands     42
## 600   2020-05-11                 Midlands     33
## 601   2020-05-12                 Midlands     45
## 602   2020-05-13                 Midlands     40
## 603   2020-05-14                 Midlands     39
## 604   2020-05-15                 Midlands     40
## 605   2020-05-16                 Midlands     34
## 606   2020-05-17                 Midlands     31
## 607   2020-05-18                 Midlands     36
## 608   2020-05-19                 Midlands     35
## 609   2020-05-20                 Midlands     36
## 610   2020-05-21                 Midlands     32
## 611   2020-05-22                 Midlands     27
## 612   2020-05-23                 Midlands     34
## 613   2020-05-24                 Midlands     20
## 614   2020-05-25                 Midlands     26
## 615   2020-05-26                 Midlands     33
## 616   2020-05-27                 Midlands     29
## 617   2020-05-28                 Midlands     28
## 618   2020-05-29                 Midlands     20
## 619   2020-05-30                 Midlands     21
## 620   2020-05-31                 Midlands     22
## 621   2020-06-01                 Midlands     20
## 622   2020-06-02                 Midlands     22
## 623   2020-06-03                 Midlands     24
## 624   2020-06-04                 Midlands     16
## 625   2020-06-05                 Midlands     21
## 626   2020-06-06                 Midlands     20
## 627   2020-06-07                 Midlands     17
## 628   2020-06-08                 Midlands     16
## 629   2020-06-09                 Midlands     18
## 630   2020-06-10                 Midlands     15
## 631   2020-06-11                 Midlands     13
## 632   2020-06-12                 Midlands     12
## 633   2020-06-13                 Midlands      6
## 634   2020-06-14                 Midlands     18
## 635   2020-06-15                 Midlands     12
## 636   2020-06-16                 Midlands     15
## 637   2020-06-17                 Midlands     11
## 638   2020-06-18                 Midlands     15
## 639   2020-06-19                 Midlands     10
## 640   2020-06-20                 Midlands     15
## 641   2020-06-21                 Midlands     14
## 642   2020-06-22                 Midlands     14
## 643   2020-06-23                 Midlands     16
## 644   2020-06-24                 Midlands     15
## 645   2020-06-25                 Midlands     18
## 646   2020-06-26                 Midlands      5
## 647   2020-06-27                 Midlands      5
## 648   2020-06-28                 Midlands      7
## 649   2020-06-29                 Midlands      6
## 650   2020-06-30                 Midlands      6
## 651   2020-07-01                 Midlands      7
## 652   2020-07-02                 Midlands     10
## 653   2020-07-03                 Midlands      3
## 654   2020-07-04                 Midlands      4
## 655   2020-07-05                 Midlands      6
## 656   2020-07-06                 Midlands      5
## 657   2020-07-07                 Midlands      3
## 658   2020-07-08                 Midlands      5
## 659   2020-07-09                 Midlands      9
## 660   2020-07-10                 Midlands      3
## 661   2020-07-11                 Midlands      0
## 662   2020-07-12                 Midlands      5
## 663   2020-07-13                 Midlands      1
## 664   2020-07-14                 Midlands      1
## 665   2020-07-15                 Midlands      6
## 666   2020-07-16                 Midlands      2
## 667   2020-07-17                 Midlands      3
## 668   2020-07-18                 Midlands      3
## 669   2020-07-19                 Midlands      3
## 670   2020-07-20                 Midlands      3
## 671   2020-07-21                 Midlands      1
## 672   2020-07-22                 Midlands      2
## 673   2020-07-23                 Midlands      6
## 674   2020-07-24                 Midlands      1
## 675   2020-07-25                 Midlands      4
## 676   2020-07-26                 Midlands      4
## 677   2020-07-27                 Midlands      5
## 678   2020-07-28                 Midlands      1
## 679   2020-07-29                 Midlands      1
## 680   2020-07-30                 Midlands      1
## 681   2020-07-31                 Midlands      2
## 682   2020-08-01                 Midlands      0
## 683   2020-08-02                 Midlands      1
## 684   2020-08-03                 Midlands      2
## 685   2020-08-04                 Midlands      1
## 686   2020-08-05                 Midlands      1
## 687   2020-08-06                 Midlands      0
## 688   2020-08-07                 Midlands      3
## 689   2020-08-08                 Midlands      2
## 690   2020-08-09                 Midlands      0
## 691   2020-08-10                 Midlands      0
## 692   2020-08-11                 Midlands      2
## 693   2020-08-12                 Midlands      0
## 694   2020-08-13                 Midlands      0
## 695   2020-08-14                 Midlands      0
## 696   2020-08-15                 Midlands      1
## 697   2020-08-16                 Midlands      0
## 698   2020-08-17                 Midlands      0
## 699   2020-08-18                 Midlands      0
## 700   2020-08-19                 Midlands      0
## 701   2020-08-20                 Midlands      0
## 702   2020-08-21                 Midlands      1
## 703   2020-08-22                 Midlands      0
## 704   2020-08-23                 Midlands      0
## 705   2020-08-24                 Midlands      0
## 706   2020-08-25                 Midlands      2
## 707   2020-08-26                 Midlands      3
## 708   2020-08-27                 Midlands      2
## 709   2020-08-28                 Midlands      1
## 710   2020-08-29                 Midlands      0
## 711   2020-08-30                 Midlands      2
## 712   2020-08-31                 Midlands      1
## 713   2020-09-01                 Midlands      0
## 714   2020-09-02                 Midlands      2
## 715   2020-09-03                 Midlands      0
## 716   2020-09-04                 Midlands      0
## 717   2020-09-05                 Midlands      0
## 718   2020-09-06                 Midlands      1
## 719   2020-09-07                 Midlands      1
## 720   2020-09-08                 Midlands      3
## 721   2020-09-09                 Midlands      0
## 722   2020-09-10                 Midlands      1
## 723   2020-09-11                 Midlands      1
## 724   2020-09-12                 Midlands      2
## 725   2020-09-13                 Midlands      4
## 726   2020-09-14                 Midlands      1
## 727   2020-09-15                 Midlands      2
## 728   2020-09-16                 Midlands      3
## 729   2020-09-17                 Midlands      2
## 730   2020-09-18                 Midlands      5
## 731   2020-09-19                 Midlands      2
## 732   2020-09-20                 Midlands      7
## 733   2020-09-21                 Midlands      3
## 734   2020-09-22                 Midlands      4
## 735   2020-09-23                 Midlands     10
## 736   2020-09-24                 Midlands      7
## 737   2020-09-25                 Midlands      4
## 738   2020-09-26                 Midlands      5
## 739   2020-09-27                 Midlands      9
## 740   2020-09-28                 Midlands      6
## 741   2020-09-29                 Midlands      4
## 742   2020-09-30                 Midlands      5
## 743   2020-10-01                 Midlands      8
## 744   2020-10-02                 Midlands      7
## 745   2020-10-03                 Midlands      6
## 746   2020-10-04                 Midlands      7
## 747   2020-10-05                 Midlands      6
## 748   2020-10-06                 Midlands      5
## 749   2020-10-07                 Midlands      9
## 750   2020-10-08                 Midlands      8
## 751   2020-10-09                 Midlands      7
## 752   2020-10-10                 Midlands      2
## 753   2020-10-11                 Midlands     15
## 754   2020-10-12                 Midlands      7
## 755   2020-10-13                 Midlands     16
## 756   2020-10-14                 Midlands     12
## 757   2020-10-15                 Midlands     11
## 758   2020-10-16                 Midlands     18
## 759   2020-10-17                 Midlands     25
## 760   2020-10-18                 Midlands     11
## 761   2020-10-19                 Midlands     14
## 762   2020-10-20                 Midlands     19
## 763   2020-10-21                 Midlands     15
## 764   2020-10-22                 Midlands     34
## 765   2020-10-23                 Midlands     32
## 766   2020-10-24                 Midlands     24
## 767   2020-10-25                 Midlands     30
## 768   2020-10-26                 Midlands     32
## 769   2020-10-27                 Midlands     36
## 770   2020-10-28                 Midlands     30
## 771   2020-10-29                 Midlands     42
## 772   2020-10-30                 Midlands     41
## 773   2020-10-31                 Midlands     50
## 774   2020-11-01                 Midlands     44
## 775   2020-11-02                 Midlands     57
## 776   2020-11-03                 Midlands     34
## 777   2020-11-04                 Midlands     65
## 778   2020-11-05                 Midlands     48
## 779   2020-11-06                 Midlands     43
## 780   2020-11-07                 Midlands     60
## 781   2020-11-08                 Midlands     54
## 782   2020-11-09                 Midlands     65
## 783   2020-11-10                 Midlands     68
## 784   2020-11-11                 Midlands     56
## 785   2020-11-12                 Midlands     64
## 786   2020-11-13                 Midlands     45
## 787   2020-11-14                 Midlands     62
## 788   2020-11-15                 Midlands     68
## 789   2020-11-16                 Midlands     61
## 790   2020-11-17                 Midlands     57
## 791   2020-11-18                 Midlands     67
## 792   2020-11-19                 Midlands     11
## 793   2020-03-01 North East and Yorkshire      0
## 794   2020-03-02 North East and Yorkshire      0
## 795   2020-03-03 North East and Yorkshire      0
## 796   2020-03-04 North East and Yorkshire      0
## 797   2020-03-05 North East and Yorkshire      0
## 798   2020-03-06 North East and Yorkshire      0
## 799   2020-03-07 North East and Yorkshire      0
## 800   2020-03-08 North East and Yorkshire      0
## 801   2020-03-09 North East and Yorkshire      0
## 802   2020-03-10 North East and Yorkshire      0
## 803   2020-03-11 North East and Yorkshire      0
## 804   2020-03-12 North East and Yorkshire      0
## 805   2020-03-13 North East and Yorkshire      0
## 806   2020-03-14 North East and Yorkshire      0
## 807   2020-03-15 North East and Yorkshire      2
## 808   2020-03-16 North East and Yorkshire      3
## 809   2020-03-17 North East and Yorkshire      1
## 810   2020-03-18 North East and Yorkshire      2
## 811   2020-03-19 North East and Yorkshire      6
## 812   2020-03-20 North East and Yorkshire      5
## 813   2020-03-21 North East and Yorkshire      6
## 814   2020-03-22 North East and Yorkshire      7
## 815   2020-03-23 North East and Yorkshire      9
## 816   2020-03-24 North East and Yorkshire      8
## 817   2020-03-25 North East and Yorkshire     18
## 818   2020-03-26 North East and Yorkshire     21
## 819   2020-03-27 North East and Yorkshire     28
## 820   2020-03-28 North East and Yorkshire     35
## 821   2020-03-29 North East and Yorkshire     38
## 822   2020-03-30 North East and Yorkshire     64
## 823   2020-03-31 North East and Yorkshire     60
## 824   2020-04-01 North East and Yorkshire     67
## 825   2020-04-02 North East and Yorkshire     75
## 826   2020-04-03 North East and Yorkshire    100
## 827   2020-04-04 North East and Yorkshire    105
## 828   2020-04-05 North East and Yorkshire     92
## 829   2020-04-06 North East and Yorkshire     96
## 830   2020-04-07 North East and Yorkshire    102
## 831   2020-04-08 North East and Yorkshire    107
## 832   2020-04-09 North East and Yorkshire    111
## 833   2020-04-10 North East and Yorkshire    117
## 834   2020-04-11 North East and Yorkshire     98
## 835   2020-04-12 North East and Yorkshire     84
## 836   2020-04-13 North East and Yorkshire     94
## 837   2020-04-14 North East and Yorkshire    107
## 838   2020-04-15 North East and Yorkshire     96
## 839   2020-04-16 North East and Yorkshire    103
## 840   2020-04-17 North East and Yorkshire     88
## 841   2020-04-18 North East and Yorkshire     95
## 842   2020-04-19 North East and Yorkshire     88
## 843   2020-04-20 North East and Yorkshire    100
## 844   2020-04-21 North East and Yorkshire     76
## 845   2020-04-22 North East and Yorkshire     84
## 846   2020-04-23 North East and Yorkshire     63
## 847   2020-04-24 North East and Yorkshire     72
## 848   2020-04-25 North East and Yorkshire     69
## 849   2020-04-26 North East and Yorkshire     65
## 850   2020-04-27 North East and Yorkshire     65
## 851   2020-04-28 North East and Yorkshire     57
## 852   2020-04-29 North East and Yorkshire     69
## 853   2020-04-30 North East and Yorkshire     57
## 854   2020-05-01 North East and Yorkshire     64
## 855   2020-05-02 North East and Yorkshire     48
## 856   2020-05-03 North East and Yorkshire     40
## 857   2020-05-04 North East and Yorkshire     49
## 858   2020-05-05 North East and Yorkshire     40
## 859   2020-05-06 North East and Yorkshire     51
## 860   2020-05-07 North East and Yorkshire     45
## 861   2020-05-08 North East and Yorkshire     42
## 862   2020-05-09 North East and Yorkshire     44
## 863   2020-05-10 North East and Yorkshire     40
## 864   2020-05-11 North East and Yorkshire     29
## 865   2020-05-12 North East and Yorkshire     27
## 866   2020-05-13 North East and Yorkshire     28
## 867   2020-05-14 North East and Yorkshire     31
## 868   2020-05-15 North East and Yorkshire     32
## 869   2020-05-16 North East and Yorkshire     35
## 870   2020-05-17 North East and Yorkshire     26
## 871   2020-05-18 North East and Yorkshire     30
## 872   2020-05-19 North East and Yorkshire     27
## 873   2020-05-20 North East and Yorkshire     22
## 874   2020-05-21 North East and Yorkshire     33
## 875   2020-05-22 North East and Yorkshire     22
## 876   2020-05-23 North East and Yorkshire     18
## 877   2020-05-24 North East and Yorkshire     26
## 878   2020-05-25 North East and Yorkshire     21
## 879   2020-05-26 North East and Yorkshire     21
## 880   2020-05-27 North East and Yorkshire     22
## 881   2020-05-28 North East and Yorkshire     21
## 882   2020-05-29 North East and Yorkshire     25
## 883   2020-05-30 North East and Yorkshire     20
## 884   2020-05-31 North East and Yorkshire     20
## 885   2020-06-01 North East and Yorkshire     17
## 886   2020-06-02 North East and Yorkshire     23
## 887   2020-06-03 North East and Yorkshire     23
## 888   2020-06-04 North East and Yorkshire     17
## 889   2020-06-05 North East and Yorkshire     18
## 890   2020-06-06 North East and Yorkshire     21
## 891   2020-06-07 North East and Yorkshire     14
## 892   2020-06-08 North East and Yorkshire     11
## 893   2020-06-09 North East and Yorkshire     12
## 894   2020-06-10 North East and Yorkshire     19
## 895   2020-06-11 North East and Yorkshire      7
## 896   2020-06-12 North East and Yorkshire      9
## 897   2020-06-13 North East and Yorkshire     10
## 898   2020-06-14 North East and Yorkshire     11
## 899   2020-06-15 North East and Yorkshire      9
## 900   2020-06-16 North East and Yorkshire     10
## 901   2020-06-17 North East and Yorkshire      9
## 902   2020-06-18 North East and Yorkshire     11
## 903   2020-06-19 North East and Yorkshire      6
## 904   2020-06-20 North East and Yorkshire      5
## 905   2020-06-21 North East and Yorkshire      4
## 906   2020-06-22 North East and Yorkshire      7
## 907   2020-06-23 North East and Yorkshire      8
## 908   2020-06-24 North East and Yorkshire     10
## 909   2020-06-25 North East and Yorkshire      4
## 910   2020-06-26 North East and Yorkshire      8
## 911   2020-06-27 North East and Yorkshire      4
## 912   2020-06-28 North East and Yorkshire      5
## 913   2020-06-29 North East and Yorkshire      2
## 914   2020-06-30 North East and Yorkshire      7
## 915   2020-07-01 North East and Yorkshire      1
## 916   2020-07-02 North East and Yorkshire      4
## 917   2020-07-03 North East and Yorkshire      4
## 918   2020-07-04 North East and Yorkshire      4
## 919   2020-07-05 North East and Yorkshire      3
## 920   2020-07-06 North East and Yorkshire      2
## 921   2020-07-07 North East and Yorkshire      3
## 922   2020-07-08 North East and Yorkshire      3
## 923   2020-07-09 North East and Yorkshire      0
## 924   2020-07-10 North East and Yorkshire      3
## 925   2020-07-11 North East and Yorkshire      1
## 926   2020-07-12 North East and Yorkshire      4
## 927   2020-07-13 North East and Yorkshire      1
## 928   2020-07-14 North East and Yorkshire      1
## 929   2020-07-15 North East and Yorkshire      2
## 930   2020-07-16 North East and Yorkshire      3
## 931   2020-07-17 North East and Yorkshire      1
## 932   2020-07-18 North East and Yorkshire      2
## 933   2020-07-19 North East and Yorkshire      2
## 934   2020-07-20 North East and Yorkshire      1
## 935   2020-07-21 North East and Yorkshire      1
## 936   2020-07-22 North East and Yorkshire      6
## 937   2020-07-23 North East and Yorkshire      0
## 938   2020-07-24 North East and Yorkshire      1
## 939   2020-07-25 North East and Yorkshire      5
## 940   2020-07-26 North East and Yorkshire      1
## 941   2020-07-27 North East and Yorkshire      0
## 942   2020-07-28 North East and Yorkshire      2
## 943   2020-07-29 North East and Yorkshire      1
## 944   2020-07-30 North East and Yorkshire      0
## 945   2020-07-31 North East and Yorkshire      1
## 946   2020-08-01 North East and Yorkshire      3
## 947   2020-08-02 North East and Yorkshire      2
## 948   2020-08-03 North East and Yorkshire      1
## 949   2020-08-04 North East and Yorkshire      2
## 950   2020-08-05 North East and Yorkshire      1
## 951   2020-08-06 North East and Yorkshire      4
## 952   2020-08-07 North East and Yorkshire      0
## 953   2020-08-08 North East and Yorkshire      2
## 954   2020-08-09 North East and Yorkshire      3
## 955   2020-08-10 North East and Yorkshire      3
## 956   2020-08-11 North East and Yorkshire      2
## 957   2020-08-12 North East and Yorkshire      2
## 958   2020-08-13 North East and Yorkshire      0
## 959   2020-08-14 North East and Yorkshire      1
## 960   2020-08-15 North East and Yorkshire      1
## 961   2020-08-16 North East and Yorkshire      0
## 962   2020-08-17 North East and Yorkshire      6
## 963   2020-08-18 North East and Yorkshire      1
## 964   2020-08-19 North East and Yorkshire      0
## 965   2020-08-20 North East and Yorkshire      0
## 966   2020-08-21 North East and Yorkshire      1
## 967   2020-08-22 North East and Yorkshire      1
## 968   2020-08-23 North East and Yorkshire      3
## 969   2020-08-24 North East and Yorkshire      0
## 970   2020-08-25 North East and Yorkshire      1
## 971   2020-08-26 North East and Yorkshire      2
## 972   2020-08-27 North East and Yorkshire      1
## 973   2020-08-28 North East and Yorkshire      0
## 974   2020-08-29 North East and Yorkshire      1
## 975   2020-08-30 North East and Yorkshire      0
## 976   2020-08-31 North East and Yorkshire      0
## 977   2020-09-01 North East and Yorkshire      2
## 978   2020-09-02 North East and Yorkshire      3
## 979   2020-09-03 North East and Yorkshire      1
## 980   2020-09-04 North East and Yorkshire      1
## 981   2020-09-05 North East and Yorkshire      2
## 982   2020-09-06 North East and Yorkshire      1
## 983   2020-09-07 North East and Yorkshire      0
## 984   2020-09-08 North East and Yorkshire      1
## 985   2020-09-09 North East and Yorkshire      2
## 986   2020-09-10 North East and Yorkshire      0
## 987   2020-09-11 North East and Yorkshire      3
## 988   2020-09-12 North East and Yorkshire      1
## 989   2020-09-13 North East and Yorkshire      3
## 990   2020-09-14 North East and Yorkshire      4
## 991   2020-09-15 North East and Yorkshire      3
## 992   2020-09-16 North East and Yorkshire      3
## 993   2020-09-17 North East and Yorkshire      5
## 994   2020-09-18 North East and Yorkshire      6
## 995   2020-09-19 North East and Yorkshire      2
## 996   2020-09-20 North East and Yorkshire      9
## 997   2020-09-21 North East and Yorkshire      7
## 998   2020-09-22 North East and Yorkshire      4
## 999   2020-09-23 North East and Yorkshire      6
## 1000  2020-09-24 North East and Yorkshire      3
## 1001  2020-09-25 North East and Yorkshire      5
## 1002  2020-09-26 North East and Yorkshire      7
## 1003  2020-09-27 North East and Yorkshire     10
## 1004  2020-09-28 North East and Yorkshire      6
## 1005  2020-09-29 North East and Yorkshire      7
## 1006  2020-09-30 North East and Yorkshire      7
## 1007  2020-10-01 North East and Yorkshire      8
## 1008  2020-10-02 North East and Yorkshire     16
## 1009  2020-10-03 North East and Yorkshire     12
## 1010  2020-10-04 North East and Yorkshire     13
## 1011  2020-10-05 North East and Yorkshire     10
## 1012  2020-10-06 North East and Yorkshire     15
## 1013  2020-10-07 North East and Yorkshire     13
## 1014  2020-10-08 North East and Yorkshire     16
## 1015  2020-10-09 North East and Yorkshire     10
## 1016  2020-10-10 North East and Yorkshire     16
## 1017  2020-10-11 North East and Yorkshire     16
## 1018  2020-10-12 North East and Yorkshire     15
## 1019  2020-10-13 North East and Yorkshire     20
## 1020  2020-10-14 North East and Yorkshire     20
## 1021  2020-10-15 North East and Yorkshire     23
## 1022  2020-10-16 North East and Yorkshire     24
## 1023  2020-10-17 North East and Yorkshire     32
## 1024  2020-10-18 North East and Yorkshire     21
## 1025  2020-10-19 North East and Yorkshire     32
## 1026  2020-10-20 North East and Yorkshire     35
## 1027  2020-10-21 North East and Yorkshire     42
## 1028  2020-10-22 North East and Yorkshire     33
## 1029  2020-10-23 North East and Yorkshire     30
## 1030  2020-10-24 North East and Yorkshire     33
## 1031  2020-10-25 North East and Yorkshire     33
## 1032  2020-10-26 North East and Yorkshire     43
## 1033  2020-10-27 North East and Yorkshire     44
## 1034  2020-10-28 North East and Yorkshire     38
## 1035  2020-10-29 North East and Yorkshire     48
## 1036  2020-10-30 North East and Yorkshire     45
## 1037  2020-10-31 North East and Yorkshire     54
## 1038  2020-11-01 North East and Yorkshire     46
## 1039  2020-11-02 North East and Yorkshire     49
## 1040  2020-11-03 North East and Yorkshire     45
## 1041  2020-11-04 North East and Yorkshire     56
## 1042  2020-11-05 North East and Yorkshire     51
## 1043  2020-11-06 North East and Yorkshire     54
## 1044  2020-11-07 North East and Yorkshire     72
## 1045  2020-11-08 North East and Yorkshire     55
## 1046  2020-11-09 North East and Yorkshire     81
## 1047  2020-11-10 North East and Yorkshire     59
## 1048  2020-11-11 North East and Yorkshire     57
## 1049  2020-11-12 North East and Yorkshire     70
## 1050  2020-11-13 North East and Yorkshire     71
## 1051  2020-11-14 North East and Yorkshire     64
## 1052  2020-11-15 North East and Yorkshire     71
## 1053  2020-11-16 North East and Yorkshire     44
## 1054  2020-11-17 North East and Yorkshire     57
## 1055  2020-11-18 North East and Yorkshire     64
## 1056  2020-11-19 North East and Yorkshire     15
## 1057  2020-03-01               North West      0
## 1058  2020-03-02               North West      0
## 1059  2020-03-03               North West      0
## 1060  2020-03-04               North West      0
## 1061  2020-03-05               North West      1
## 1062  2020-03-06               North West      0
## 1063  2020-03-07               North West      0
## 1064  2020-03-08               North West      1
## 1065  2020-03-09               North West      0
## 1066  2020-03-10               North West      0
## 1067  2020-03-11               North West      0
## 1068  2020-03-12               North West      2
## 1069  2020-03-13               North West      3
## 1070  2020-03-14               North West      1
## 1071  2020-03-15               North West      4
## 1072  2020-03-16               North West      2
## 1073  2020-03-17               North West      4
## 1074  2020-03-18               North West      6
## 1075  2020-03-19               North West      7
## 1076  2020-03-20               North West     10
## 1077  2020-03-21               North West     11
## 1078  2020-03-22               North West     13
## 1079  2020-03-23               North West     15
## 1080  2020-03-24               North West     21
## 1081  2020-03-25               North West     21
## 1082  2020-03-26               North West     29
## 1083  2020-03-27               North West     36
## 1084  2020-03-28               North West     28
## 1085  2020-03-29               North West     46
## 1086  2020-03-30               North West     67
## 1087  2020-03-31               North West     52
## 1088  2020-04-01               North West     86
## 1089  2020-04-02               North West     96
## 1090  2020-04-03               North West     95
## 1091  2020-04-04               North West     98
## 1092  2020-04-05               North West    102
## 1093  2020-04-06               North West    100
## 1094  2020-04-07               North West    135
## 1095  2020-04-08               North West    127
## 1096  2020-04-09               North West    119
## 1097  2020-04-10               North West    117
## 1098  2020-04-11               North West    138
## 1099  2020-04-12               North West    125
## 1100  2020-04-13               North West    129
## 1101  2020-04-14               North West    130
## 1102  2020-04-15               North West    114
## 1103  2020-04-16               North West    135
## 1104  2020-04-17               North West     98
## 1105  2020-04-18               North West    113
## 1106  2020-04-19               North West     71
## 1107  2020-04-20               North West     83
## 1108  2020-04-21               North West     76
## 1109  2020-04-22               North West     86
## 1110  2020-04-23               North West     85
## 1111  2020-04-24               North West     66
## 1112  2020-04-25               North West     66
## 1113  2020-04-26               North West     55
## 1114  2020-04-27               North West     54
## 1115  2020-04-28               North West     57
## 1116  2020-04-29               North West     63
## 1117  2020-04-30               North West     60
## 1118  2020-05-01               North West     45
## 1119  2020-05-02               North West     56
## 1120  2020-05-03               North West     55
## 1121  2020-05-04               North West     48
## 1122  2020-05-05               North West     48
## 1123  2020-05-06               North West     44
## 1124  2020-05-07               North West     49
## 1125  2020-05-08               North West     42
## 1126  2020-05-09               North West     31
## 1127  2020-05-10               North West     42
## 1128  2020-05-11               North West     35
## 1129  2020-05-12               North West     38
## 1130  2020-05-13               North West     25
## 1131  2020-05-14               North West     26
## 1132  2020-05-15               North West     33
## 1133  2020-05-16               North West     32
## 1134  2020-05-17               North West     24
## 1135  2020-05-18               North West     31
## 1136  2020-05-19               North West     35
## 1137  2020-05-20               North West     27
## 1138  2020-05-21               North West     28
## 1139  2020-05-22               North West     26
## 1140  2020-05-23               North West     31
## 1141  2020-05-24               North West     26
## 1142  2020-05-25               North West     31
## 1143  2020-05-26               North West     27
## 1144  2020-05-27               North West     27
## 1145  2020-05-28               North West     28
## 1146  2020-05-29               North West     20
## 1147  2020-05-30               North West     19
## 1148  2020-05-31               North West     13
## 1149  2020-06-01               North West     12
## 1150  2020-06-02               North West     27
## 1151  2020-06-03               North West     22
## 1152  2020-06-04               North West     22
## 1153  2020-06-05               North West     16
## 1154  2020-06-06               North West     26
## 1155  2020-06-07               North West     20
## 1156  2020-06-08               North West     23
## 1157  2020-06-09               North West     17
## 1158  2020-06-10               North West     16
## 1159  2020-06-11               North West     16
## 1160  2020-06-12               North West     11
## 1161  2020-06-13               North West     10
## 1162  2020-06-14               North West     15
## 1163  2020-06-15               North West     16
## 1164  2020-06-16               North West     16
## 1165  2020-06-17               North West     13
## 1166  2020-06-18               North West     14
## 1167  2020-06-19               North West      7
## 1168  2020-06-20               North West     11
## 1169  2020-06-21               North West      8
## 1170  2020-06-22               North West     11
## 1171  2020-06-23               North West     13
## 1172  2020-06-24               North West     13
## 1173  2020-06-25               North West     15
## 1174  2020-06-26               North West      6
## 1175  2020-06-27               North West      7
## 1176  2020-06-28               North West      9
## 1177  2020-06-29               North West      9
## 1178  2020-06-30               North West      7
## 1179  2020-07-01               North West      3
## 1180  2020-07-02               North West      6
## 1181  2020-07-03               North West      7
## 1182  2020-07-04               North West      4
## 1183  2020-07-05               North West      6
## 1184  2020-07-06               North West      9
## 1185  2020-07-07               North West      8
## 1186  2020-07-08               North West      5
## 1187  2020-07-09               North West     10
## 1188  2020-07-10               North West      2
## 1189  2020-07-11               North West      5
## 1190  2020-07-12               North West      0
## 1191  2020-07-13               North West      6
## 1192  2020-07-14               North West      4
## 1193  2020-07-15               North West      5
## 1194  2020-07-16               North West      2
## 1195  2020-07-17               North West      4
## 1196  2020-07-18               North West      5
## 1197  2020-07-19               North West      3
## 1198  2020-07-20               North West      0
## 1199  2020-07-21               North West      2
## 1200  2020-07-22               North West      3
## 1201  2020-07-23               North West      3
## 1202  2020-07-24               North West      1
## 1203  2020-07-25               North West      1
## 1204  2020-07-26               North West      3
## 1205  2020-07-27               North West      1
## 1206  2020-07-28               North West      1
## 1207  2020-07-29               North West      2
## 1208  2020-07-30               North West      2
## 1209  2020-07-31               North West      0
## 1210  2020-08-01               North West      2
## 1211  2020-08-02               North West      1
## 1212  2020-08-03               North West      8
## 1213  2020-08-04               North West      3
## 1214  2020-08-05               North West      2
## 1215  2020-08-06               North West      2
## 1216  2020-08-07               North West      2
## 1217  2020-08-08               North West      2
## 1218  2020-08-09               North West      3
## 1219  2020-08-10               North West      2
## 1220  2020-08-11               North West      3
## 1221  2020-08-12               North West      0
## 1222  2020-08-13               North West      2
## 1223  2020-08-14               North West      2
## 1224  2020-08-15               North West      6
## 1225  2020-08-16               North West      2
## 1226  2020-08-17               North West      1
## 1227  2020-08-18               North West      2
## 1228  2020-08-19               North West      1
## 1229  2020-08-20               North West      1
## 1230  2020-08-21               North West      4
## 1231  2020-08-22               North West      3
## 1232  2020-08-23               North West      5
## 1233  2020-08-24               North West      4
## 1234  2020-08-25               North West      3
## 1235  2020-08-26               North West      4
## 1236  2020-08-27               North West      1
## 1237  2020-08-28               North West      2
## 1238  2020-08-29               North West      0
## 1239  2020-08-30               North West      2
## 1240  2020-08-31               North West      3
## 1241  2020-09-01               North West      0
## 1242  2020-09-02               North West      2
## 1243  2020-09-03               North West      1
## 1244  2020-09-04               North West      3
## 1245  2020-09-05               North West      6
## 1246  2020-09-06               North West      1
## 1247  2020-09-07               North West      8
## 1248  2020-09-08               North West      6
## 1249  2020-09-09               North West      5
## 1250  2020-09-10               North West      5
## 1251  2020-09-11               North West      1
## 1252  2020-09-12               North West      4
## 1253  2020-09-13               North West      2
## 1254  2020-09-14               North West      4
## 1255  2020-09-15               North West      4
## 1256  2020-09-16               North West      6
## 1257  2020-09-17               North West      7
## 1258  2020-09-18               North West      6
## 1259  2020-09-19               North West      3
## 1260  2020-09-20               North West      2
## 1261  2020-09-21               North West      2
## 1262  2020-09-22               North West      9
## 1263  2020-09-23               North West     14
## 1264  2020-09-24               North West     10
## 1265  2020-09-25               North West      8
## 1266  2020-09-26               North West     14
## 1267  2020-09-27               North West     11
## 1268  2020-09-28               North West     15
## 1269  2020-09-29               North West     12
## 1270  2020-09-30               North West     17
## 1271  2020-10-01               North West     17
## 1272  2020-10-02               North West     20
## 1273  2020-10-03               North West     15
## 1274  2020-10-04               North West     15
## 1275  2020-10-05               North West     15
## 1276  2020-10-06               North West     20
## 1277  2020-10-07               North West     20
## 1278  2020-10-08               North West     22
## 1279  2020-10-09               North West     23
## 1280  2020-10-10               North West     31
## 1281  2020-10-11               North West     31
## 1282  2020-10-12               North West     35
## 1283  2020-10-13               North West     26
## 1284  2020-10-14               North West     35
## 1285  2020-10-15               North West     36
## 1286  2020-10-16               North West     34
## 1287  2020-10-17               North West     52
## 1288  2020-10-18               North West     40
## 1289  2020-10-19               North West     43
## 1290  2020-10-20               North West     48
## 1291  2020-10-21               North West     51
## 1292  2020-10-22               North West     49
## 1293  2020-10-23               North West     50
## 1294  2020-10-24               North West     50
## 1295  2020-10-25               North West     62
## 1296  2020-10-26               North West     53
## 1297  2020-10-27               North West     48
## 1298  2020-10-28               North West     57
## 1299  2020-10-29               North West     72
## 1300  2020-10-30               North West     68
## 1301  2020-10-31               North West     63
## 1302  2020-11-01               North West     73
## 1303  2020-11-02               North West     63
## 1304  2020-11-03               North West     76
## 1305  2020-11-04               North West     64
## 1306  2020-11-05               North West     66
## 1307  2020-11-06               North West     72
## 1308  2020-11-07               North West     73
## 1309  2020-11-08               North West     82
## 1310  2020-11-09               North West     78
## 1311  2020-11-10               North West     65
## 1312  2020-11-11               North West     58
## 1313  2020-11-12               North West     63
## 1314  2020-11-13               North West     72
## 1315  2020-11-14               North West     58
## 1316  2020-11-15               North West     71
## 1317  2020-11-16               North West     71
## 1318  2020-11-17               North West     62
## 1319  2020-11-18               North West     46
## 1320  2020-11-19               North West     14
## 1321  2020-03-01               South East      0
## 1322  2020-03-02               South East      0
## 1323  2020-03-03               South East      1
## 1324  2020-03-04               South East      0
## 1325  2020-03-05               South East      1
## 1326  2020-03-06               South East      0
## 1327  2020-03-07               South East      0
## 1328  2020-03-08               South East      1
## 1329  2020-03-09               South East      1
## 1330  2020-03-10               South East      1
## 1331  2020-03-11               South East      1
## 1332  2020-03-12               South East      0
## 1333  2020-03-13               South East      1
## 1334  2020-03-14               South East      1
## 1335  2020-03-15               South East      5
## 1336  2020-03-16               South East      8
## 1337  2020-03-17               South East      7
## 1338  2020-03-18               South East     10
## 1339  2020-03-19               South East      9
## 1340  2020-03-20               South East     13
## 1341  2020-03-21               South East      7
## 1342  2020-03-22               South East     25
## 1343  2020-03-23               South East     20
## 1344  2020-03-24               South East     22
## 1345  2020-03-25               South East     29
## 1346  2020-03-26               South East     35
## 1347  2020-03-27               South East     36
## 1348  2020-03-28               South East     36
## 1349  2020-03-29               South East     55
## 1350  2020-03-30               South East     58
## 1351  2020-03-31               South East     65
## 1352  2020-04-01               South East     66
## 1353  2020-04-02               South East     55
## 1354  2020-04-03               South East     72
## 1355  2020-04-04               South East     80
## 1356  2020-04-05               South East     82
## 1357  2020-04-06               South East     88
## 1358  2020-04-07               South East    100
## 1359  2020-04-08               South East     83
## 1360  2020-04-09               South East    104
## 1361  2020-04-10               South East     88
## 1362  2020-04-11               South East     88
## 1363  2020-04-12               South East     88
## 1364  2020-04-13               South East     84
## 1365  2020-04-14               South East     65
## 1366  2020-04-15               South East     72
## 1367  2020-04-16               South East     56
## 1368  2020-04-17               South East     86
## 1369  2020-04-18               South East     57
## 1370  2020-04-19               South East     70
## 1371  2020-04-20               South East     87
## 1372  2020-04-21               South East     51
## 1373  2020-04-22               South East     54
## 1374  2020-04-23               South East     57
## 1375  2020-04-24               South East     64
## 1376  2020-04-25               South East     51
## 1377  2020-04-26               South East     51
## 1378  2020-04-27               South East     41
## 1379  2020-04-28               South East     40
## 1380  2020-04-29               South East     47
## 1381  2020-04-30               South East     29
## 1382  2020-05-01               South East     37
## 1383  2020-05-02               South East     36
## 1384  2020-05-03               South East     17
## 1385  2020-05-04               South East     35
## 1386  2020-05-05               South East     29
## 1387  2020-05-06               South East     25
## 1388  2020-05-07               South East     27
## 1389  2020-05-08               South East     26
## 1390  2020-05-09               South East     28
## 1391  2020-05-10               South East     19
## 1392  2020-05-11               South East     25
## 1393  2020-05-12               South East     27
## 1394  2020-05-13               South East     18
## 1395  2020-05-14               South East     32
## 1396  2020-05-15               South East     25
## 1397  2020-05-16               South East     22
## 1398  2020-05-17               South East     18
## 1399  2020-05-18               South East     22
## 1400  2020-05-19               South East     12
## 1401  2020-05-20               South East     22
## 1402  2020-05-21               South East     15
## 1403  2020-05-22               South East     17
## 1404  2020-05-23               South East     21
## 1405  2020-05-24               South East     17
## 1406  2020-05-25               South East     13
## 1407  2020-05-26               South East     19
## 1408  2020-05-27               South East     19
## 1409  2020-05-28               South East     12
## 1410  2020-05-29               South East     22
## 1411  2020-05-30               South East      8
## 1412  2020-05-31               South East     12
## 1413  2020-06-01               South East     11
## 1414  2020-06-02               South East     13
## 1415  2020-06-03               South East     18
## 1416  2020-06-04               South East     11
## 1417  2020-06-05               South East     11
## 1418  2020-06-06               South East     10
## 1419  2020-06-07               South East     12
## 1420  2020-06-08               South East      8
## 1421  2020-06-09               South East     10
## 1422  2020-06-10               South East     11
## 1423  2020-06-11               South East      5
## 1424  2020-06-12               South East      6
## 1425  2020-06-13               South East      7
## 1426  2020-06-14               South East      7
## 1427  2020-06-15               South East      8
## 1428  2020-06-16               South East     14
## 1429  2020-06-17               South East      9
## 1430  2020-06-18               South East      4
## 1431  2020-06-19               South East      7
## 1432  2020-06-20               South East      5
## 1433  2020-06-21               South East      3
## 1434  2020-06-22               South East      2
## 1435  2020-06-23               South East      9
## 1436  2020-06-24               South East      7
## 1437  2020-06-25               South East      5
## 1438  2020-06-26               South East      8
## 1439  2020-06-27               South East      9
## 1440  2020-06-28               South East      6
## 1441  2020-06-29               South East      5
## 1442  2020-06-30               South East      5
## 1443  2020-07-01               South East      2
## 1444  2020-07-02               South East      8
## 1445  2020-07-03               South East      3
## 1446  2020-07-04               South East      6
## 1447  2020-07-05               South East      5
## 1448  2020-07-06               South East      4
## 1449  2020-07-07               South East      6
## 1450  2020-07-08               South East      3
## 1451  2020-07-09               South East      7
## 1452  2020-07-10               South East      3
## 1453  2020-07-11               South East      4
## 1454  2020-07-12               South East      4
## 1455  2020-07-13               South East      5
## 1456  2020-07-14               South East      5
## 1457  2020-07-15               South East      6
## 1458  2020-07-16               South East      3
## 1459  2020-07-17               South East      1
## 1460  2020-07-18               South East      5
## 1461  2020-07-19               South East      2
## 1462  2020-07-20               South East      6
## 1463  2020-07-21               South East      4
## 1464  2020-07-22               South East      2
## 1465  2020-07-23               South East      3
## 1466  2020-07-24               South East      1
## 1467  2020-07-25               South East      1
## 1468  2020-07-26               South East      3
## 1469  2020-07-27               South East      1
## 1470  2020-07-28               South East      3
## 1471  2020-07-29               South East      2
## 1472  2020-07-30               South East      3
## 1473  2020-07-31               South East      1
## 1474  2020-08-01               South East      2
## 1475  2020-08-02               South East      4
## 1476  2020-08-03               South East      0
## 1477  2020-08-04               South East      0
## 1478  2020-08-05               South East      0
## 1479  2020-08-06               South East      2
## 1480  2020-08-07               South East      0
## 1481  2020-08-08               South East      2
## 1482  2020-08-09               South East      0
## 1483  2020-08-10               South East      2
## 1484  2020-08-11               South East      1
## 1485  2020-08-12               South East      1
## 1486  2020-08-13               South East      0
## 1487  2020-08-14               South East      0
## 1488  2020-08-15               South East      2
## 1489  2020-08-16               South East      1
## 1490  2020-08-17               South East      0
## 1491  2020-08-18               South East      2
## 1492  2020-08-19               South East      1
## 1493  2020-08-20               South East      0
## 1494  2020-08-21               South East      0
## 1495  2020-08-22               South East      0
## 1496  2020-08-23               South East      1
## 1497  2020-08-24               South East      0
## 1498  2020-08-25               South East      1
## 1499  2020-08-26               South East      0
## 1500  2020-08-27               South East      1
## 1501  2020-08-28               South East      2
## 1502  2020-08-29               South East      1
## 1503  2020-08-30               South East      0
## 1504  2020-08-31               South East      2
## 1505  2020-09-01               South East      1
## 1506  2020-09-02               South East      1
## 1507  2020-09-03               South East      0
## 1508  2020-09-04               South East      1
## 1509  2020-09-05               South East      0
## 1510  2020-09-06               South East      1
## 1511  2020-09-07               South East      0
## 1512  2020-09-08               South East      0
## 1513  2020-09-09               South East      0
## 1514  2020-09-10               South East      1
## 1515  2020-09-11               South East      1
## 1516  2020-09-12               South East      0
## 1517  2020-09-13               South East      3
## 1518  2020-09-14               South East      1
## 1519  2020-09-15               South East      2
## 1520  2020-09-16               South East      2
## 1521  2020-09-17               South East      3
## 1522  2020-09-18               South East      1
## 1523  2020-09-19               South East      1
## 1524  2020-09-20               South East      0
## 1525  2020-09-21               South East      3
## 1526  2020-09-22               South East      0
## 1527  2020-09-23               South East      2
## 1528  2020-09-24               South East      0
## 1529  2020-09-25               South East      3
## 1530  2020-09-26               South East      2
## 1531  2020-09-27               South East      2
## 1532  2020-09-28               South East      6
## 1533  2020-09-29               South East      3
## 1534  2020-09-30               South East      4
## 1535  2020-10-01               South East      4
## 1536  2020-10-02               South East      2
## 1537  2020-10-03               South East      1
## 1538  2020-10-04               South East      1
## 1539  2020-10-05               South East      2
## 1540  2020-10-06               South East      1
## 1541  2020-10-07               South East      4
## 1542  2020-10-08               South East      1
## 1543  2020-10-09               South East      1
## 1544  2020-10-10               South East      3
## 1545  2020-10-11               South East      3
## 1546  2020-10-12               South East      4
## 1547  2020-10-13               South East      2
## 1548  2020-10-14               South East      2
## 1549  2020-10-15               South East      3
## 1550  2020-10-16               South East      2
## 1551  2020-10-17               South East      3
## 1552  2020-10-18               South East      4
## 1553  2020-10-19               South East      7
## 1554  2020-10-20               South East      8
## 1555  2020-10-21               South East      9
## 1556  2020-10-22               South East      5
## 1557  2020-10-23               South East      7
## 1558  2020-10-24               South East      5
## 1559  2020-10-25               South East      9
## 1560  2020-10-26               South East     13
## 1561  2020-10-27               South East     10
## 1562  2020-10-28               South East     10
## 1563  2020-10-29               South East      7
## 1564  2020-10-30               South East      6
## 1565  2020-10-31               South East     15
## 1566  2020-11-01               South East     18
## 1567  2020-11-02               South East     13
## 1568  2020-11-03               South East     16
## 1569  2020-11-04               South East     10
## 1570  2020-11-05               South East     10
## 1571  2020-11-06               South East     16
## 1572  2020-11-07               South East     17
## 1573  2020-11-08               South East     18
## 1574  2020-11-09               South East     19
## 1575  2020-11-10               South East     20
## 1576  2020-11-11               South East     19
## 1577  2020-11-12               South East     20
## 1578  2020-11-13               South East     11
## 1579  2020-11-14               South East     22
## 1580  2020-11-15               South East     22
## 1581  2020-11-16               South East     22
## 1582  2020-11-17               South East     21
## 1583  2020-11-18               South East     13
## 1584  2020-11-19               South East      3
## 1585  2020-03-01               South West      0
## 1586  2020-03-02               South West      0
## 1587  2020-03-03               South West      0
## 1588  2020-03-04               South West      0
## 1589  2020-03-05               South West      0
## 1590  2020-03-06               South West      0
## 1591  2020-03-07               South West      0
## 1592  2020-03-08               South West      0
## 1593  2020-03-09               South West      0
## 1594  2020-03-10               South West      0
## 1595  2020-03-11               South West      1
## 1596  2020-03-12               South West      0
## 1597  2020-03-13               South West      0
## 1598  2020-03-14               South West      1
## 1599  2020-03-15               South West      0
## 1600  2020-03-16               South West      0
## 1601  2020-03-17               South West      2
## 1602  2020-03-18               South West      2
## 1603  2020-03-19               South West      4
## 1604  2020-03-20               South West      3
## 1605  2020-03-21               South West      6
## 1606  2020-03-22               South West      7
## 1607  2020-03-23               South West      8
## 1608  2020-03-24               South West      7
## 1609  2020-03-25               South West      9
## 1610  2020-03-26               South West     11
## 1611  2020-03-27               South West     13
## 1612  2020-03-28               South West     21
## 1613  2020-03-29               South West     18
## 1614  2020-03-30               South West     23
## 1615  2020-03-31               South West     23
## 1616  2020-04-01               South West     21
## 1617  2020-04-02               South West     23
## 1618  2020-04-03               South West     30
## 1619  2020-04-04               South West     42
## 1620  2020-04-05               South West     32
## 1621  2020-04-06               South West     34
## 1622  2020-04-07               South West     39
## 1623  2020-04-08               South West     47
## 1624  2020-04-09               South West     24
## 1625  2020-04-10               South West     46
## 1626  2020-04-11               South West     43
## 1627  2020-04-12               South West     23
## 1628  2020-04-13               South West     27
## 1629  2020-04-14               South West     24
## 1630  2020-04-15               South West     32
## 1631  2020-04-16               South West     29
## 1632  2020-04-17               South West     33
## 1633  2020-04-18               South West     25
## 1634  2020-04-19               South West     31
## 1635  2020-04-20               South West     26
## 1636  2020-04-21               South West     26
## 1637  2020-04-22               South West     23
## 1638  2020-04-23               South West     17
## 1639  2020-04-24               South West     19
## 1640  2020-04-25               South West     15
## 1641  2020-04-26               South West     27
## 1642  2020-04-27               South West     13
## 1643  2020-04-28               South West     17
## 1644  2020-04-29               South West     15
## 1645  2020-04-30               South West     26
## 1646  2020-05-01               South West      6
## 1647  2020-05-02               South West      7
## 1648  2020-05-03               South West     10
## 1649  2020-05-04               South West     17
## 1650  2020-05-05               South West     14
## 1651  2020-05-06               South West     19
## 1652  2020-05-07               South West     16
## 1653  2020-05-08               South West      6
## 1654  2020-05-09               South West     11
## 1655  2020-05-10               South West      5
## 1656  2020-05-11               South West      8
## 1657  2020-05-12               South West      7
## 1658  2020-05-13               South West      7
## 1659  2020-05-14               South West      6
## 1660  2020-05-15               South West      4
## 1661  2020-05-16               South West      4
## 1662  2020-05-17               South West      6
## 1663  2020-05-18               South West      4
## 1664  2020-05-19               South West      6
## 1665  2020-05-20               South West      1
## 1666  2020-05-21               South West      9
## 1667  2020-05-22               South West      7
## 1668  2020-05-23               South West      6
## 1669  2020-05-24               South West      3
## 1670  2020-05-25               South West      8
## 1671  2020-05-26               South West     11
## 1672  2020-05-27               South West      5
## 1673  2020-05-28               South West     10
## 1674  2020-05-29               South West      7
## 1675  2020-05-30               South West      3
## 1676  2020-05-31               South West      2
## 1677  2020-06-01               South West      7
## 1678  2020-06-02               South West      2
## 1679  2020-06-03               South West      7
## 1680  2020-06-04               South West      2
## 1681  2020-06-05               South West      2
## 1682  2020-06-06               South West      1
## 1683  2020-06-07               South West      3
## 1684  2020-06-08               South West      3
## 1685  2020-06-09               South West      0
## 1686  2020-06-10               South West      1
## 1687  2020-06-11               South West      2
## 1688  2020-06-12               South West      2
## 1689  2020-06-13               South West      2
## 1690  2020-06-14               South West      0
## 1691  2020-06-15               South West      2
## 1692  2020-06-16               South West      2
## 1693  2020-06-17               South West      0
## 1694  2020-06-18               South West      0
## 1695  2020-06-19               South West      0
## 1696  2020-06-20               South West      2
## 1697  2020-06-21               South West      0
## 1698  2020-06-22               South West      1
## 1699  2020-06-23               South West      1
## 1700  2020-06-24               South West      1
## 1701  2020-06-25               South West      0
## 1702  2020-06-26               South West      3
## 1703  2020-06-27               South West      0
## 1704  2020-06-28               South West      0
## 1705  2020-06-29               South West      1
## 1706  2020-06-30               South West      0
## 1707  2020-07-01               South West      0
## 1708  2020-07-02               South West      0
## 1709  2020-07-03               South West      0
## 1710  2020-07-04               South West      0
## 1711  2020-07-05               South West      1
## 1712  2020-07-06               South West      0
## 1713  2020-07-07               South West      0
## 1714  2020-07-08               South West      2
## 1715  2020-07-09               South West      0
## 1716  2020-07-10               South West      1
## 1717  2020-07-11               South West      0
## 1718  2020-07-12               South West      0
## 1719  2020-07-13               South West      1
## 1720  2020-07-14               South West      0
## 1721  2020-07-15               South West      0
## 1722  2020-07-16               South West      0
## 1723  2020-07-17               South West      1
## 1724  2020-07-18               South West      0
## 1725  2020-07-19               South West      0
## 1726  2020-07-20               South West      0
## 1727  2020-07-21               South West      0
## 1728  2020-07-22               South West      0
## 1729  2020-07-23               South West      0
## 1730  2020-07-24               South West      0
## 1731  2020-07-25               South West      0
## 1732  2020-07-26               South West      0
## 1733  2020-07-27               South West      0
## 1734  2020-07-28               South West      0
## 1735  2020-07-29               South West      0
## 1736  2020-07-30               South West      1
## 1737  2020-07-31               South West      0
## 1738  2020-08-01               South West      0
## 1739  2020-08-02               South West      0
## 1740  2020-08-03               South West      0
## 1741  2020-08-04               South West      0
## 1742  2020-08-05               South West      0
## 1743  2020-08-06               South West      0
## 1744  2020-08-07               South West      0
## 1745  2020-08-08               South West      0
## 1746  2020-08-09               South West      0
## 1747  2020-08-10               South West      0
## 1748  2020-08-11               South West      0
## 1749  2020-08-12               South West      0
## 1750  2020-08-13               South West      0
## 1751  2020-08-14               South West      1
## 1752  2020-08-15               South West      0
## 1753  2020-08-16               South West      0
## 1754  2020-08-17               South West      2
## 1755  2020-08-18               South West      0
## 1756  2020-08-19               South West      0
## 1757  2020-08-20               South West      0
## 1758  2020-08-21               South West      0
## 1759  2020-08-22               South West      0
## 1760  2020-08-23               South West      0
## 1761  2020-08-24               South West      0
## 1762  2020-08-25               South West      1
## 1763  2020-08-26               South West      0
## 1764  2020-08-27               South West      1
## 1765  2020-08-28               South West      0
## 1766  2020-08-29               South West      0
## 1767  2020-08-30               South West      0
## 1768  2020-08-31               South West      0
## 1769  2020-09-01               South West      0
## 1770  2020-09-02               South West      0
## 1771  2020-09-03               South West      0
## 1772  2020-09-04               South West      0
## 1773  2020-09-05               South West      0
## 1774  2020-09-06               South West      0
## 1775  2020-09-07               South West      0
## 1776  2020-09-08               South West      1
## 1777  2020-09-09               South West      0
## 1778  2020-09-10               South West      0
## 1779  2020-09-11               South West      0
## 1780  2020-09-12               South West      0
## 1781  2020-09-13               South West      1
## 1782  2020-09-14               South West      0
## 1783  2020-09-15               South West      0
## 1784  2020-09-16               South West      0
## 1785  2020-09-17               South West      1
## 1786  2020-09-18               South West      0
## 1787  2020-09-19               South West      0
## 1788  2020-09-20               South West      1
## 1789  2020-09-21               South West      0
## 1790  2020-09-22               South West      0
## 1791  2020-09-23               South West      0
## 1792  2020-09-24               South West      1
## 1793  2020-09-25               South West      0
## 1794  2020-09-26               South West      0
## 1795  2020-09-27               South West      0
## 1796  2020-09-28               South West      0
## 1797  2020-09-29               South West      0
## 1798  2020-09-30               South West      0
## 1799  2020-10-01               South West      0
## 1800  2020-10-02               South West      1
## 1801  2020-10-03               South West      0
## 1802  2020-10-04               South West      0
## 1803  2020-10-05               South West      0
## 1804  2020-10-06               South West      1
## 1805  2020-10-07               South West      0
## 1806  2020-10-08               South West      1
## 1807  2020-10-09               South West      1
## 1808  2020-10-10               South West      0
## 1809  2020-10-11               South West      4
## 1810  2020-10-12               South West      2
## 1811  2020-10-13               South West      0
## 1812  2020-10-14               South West      3
## 1813  2020-10-15               South West      1
## 1814  2020-10-16               South West      2
## 1815  2020-10-17               South West      8
## 1816  2020-10-18               South West      2
## 1817  2020-10-19               South West      2
## 1818  2020-10-20               South West      3
## 1819  2020-10-21               South West      6
## 1820  2020-10-22               South West      6
## 1821  2020-10-23               South West      5
## 1822  2020-10-24               South West      5
## 1823  2020-10-25               South West      5
## 1824  2020-10-26               South West      7
## 1825  2020-10-27               South West      6
## 1826  2020-10-28               South West      7
## 1827  2020-10-29               South West     10
## 1828  2020-10-30               South West      8
## 1829  2020-10-31               South West      4
## 1830  2020-11-01               South West      5
## 1831  2020-11-02               South West     11
## 1832  2020-11-03               South West      6
## 1833  2020-11-04               South West      8
## 1834  2020-11-05               South West      5
## 1835  2020-11-06               South West     11
## 1836  2020-11-07               South West      9
## 1837  2020-11-08               South West     10
## 1838  2020-11-09               South West     11
## 1839  2020-11-10               South West      6
## 1840  2020-11-11               South West     13
## 1841  2020-11-12               South West     15
## 1842  2020-11-13               South West      9
## 1843  2020-11-14               South West      8
## 1844  2020-11-15               South West     14
## 1845  2020-11-16               South West     14
## 1846  2020-11-17               South West     13
## 1847  2020-11-18               South West     18
## 1848  2020-11-19               South West      0

1.5 Completion date

We extract the completion date from the NHS Pathways file timestamp:


database_date <- attr(x, "timestamp")
database_date
## [1] "2020-11-19"

The completion date of the NHS Pathways data is Thursday 19 Nov 2020.

1.6 Auxiliary functions

These are functions which will be used further in the analyses.

Function to estimate the generalised R-squared as the proportion of deviance explained by a given model:


## Function to calculate R2 for Poisson model
## not adjusted for model complexity but all models have the same DF here

Rsq <- function(x) {
  1 - (x$deviance / x$null.deviance)
}

Function to extract growth rates per region as well as halving times, and the associated 95% confidence intervals:


## function to extract the coefficients, find the level of the intercept,
## reconstruct the values of r, get confidence intervals

get_r <- function(model) {
  ##  extract coefficients and conf int
  out <- data.frame(r = coef(model))  %>%
    rownames_to_column("var") %>% 
    cbind(confint(model)) %>%
    filter(!grepl("day_of_week", var)) %>% 
    filter(grepl("day", var)) %>%
    rename(lower_95 = "2.5 %",
           upper_95 = "97.5 %") %>%
    mutate(var = sub("day:", "", var))
  
  ## reconstruct values: intercept + region-coefficient
  for (i in 2:nrow(out)) {
    out[i, -1] <- out[1, -1] + out[i, -1]
  }
  
  ## find the name of the intercept, restore regions names
  out <- out %>%
    mutate(nhs_region = model$xlevels$nhs_region) %>%
    select(nhs_region, everything(), -var)
  
  ## find halving times
  halving <- log(0.5) / out[,-1] %>%
    rename(halving_t = r,
           halving_t_lower_95 = lower_95,
           halving_t_upper_95 = upper_95)
  
  ## set halving times with exclusion intervals to NA
  no_halving <- out$lower_95 < 0 & out$upper_95 > 0
  halving[no_halving, ] <- NA_real_
  
  ## return all data
  cbind(out, halving)
  
}

Functions used in the correlation analysis between NHS Pathways reports and deaths:

## Function to calculate Pearson's correlation between deaths and lagged
## reports. Note that `pearson` can be replaced with `spearman` for rank
## correlation.

getcor <- function(x, ndx) {
  return(cor(x$deaths[ndx],
             x$note_lag[ndx],
             use = "complete.obs",
             method = "pearson"))
}

## Catch if sample size throws an error
getcor2 <- possibly(getcor, otherwise = NA)

getboot <- function(x) {
  result <- boot::boot.ci(boot::boot(x, getcor2, R = 1000), 
                           type = "bca")
  return(data.frame(n = sum(!is.na(x$note_lag) & !is.na(x$deaths)),
                    r = result$t0,
                    r_low = result$bca[4],
                    r_hi = result$bca[5]))
}

Function to classify the day of the week into weekend, Monday, and the rest:


## Fn to add day of week
day_of_week <- function(df) {
  df %>% 
    dplyr::mutate(day_of_week = lubridate::wday(date, label = TRUE)) %>% 
    dplyr::mutate(day_of_week = dplyr::case_when(
      day_of_week %in% c("Sat", "Sun") ~ "weekend",
      day_of_week %in% c("Mon") ~ "monday",
      !(day_of_week %in% c("Sat", "Sun", "Mon")) ~ "rest_of_week"
    ) %>% 
      factor(levels = c("rest_of_week", "monday", "weekend")))
}

Custom color palettes, color scales, and vectors of colors:


pal <- c("#006212",
         "#ae3cab",
         "#00db90",
         "#960c00",
         "#55aaff",
         "#ff7e78",
         "#00388d")

age.pal <- viridis::viridis(3,begin = 0.1, end = 0.7)

3 Comparison with deaths time series

3.1 Outline

We want to explore the correlation between NHS Pathways reports and deaths, and assess the potential for reports to be used as an early warning system for disease resurgence.

Death data are publically available. We truncate the time series to avoid bias from reporting delay - we assume a conservative delay of three weeks.

3.2 Lagged correlation

We calculate Pearson’s correlation coefficient between deaths and NHS Pathways notifications using different lags. Confidence intervals are obtained using bootstrap. Note that results were also confirmed using Spearman’s rank correlation.

First we join the NHS Pathways and death data, and aggregate over all England:

## truncate death data for reporting delay
trunc_date <- max(dth$date_report) - delay_max

dth_trunc <- dth %>%
  rename(date = date_report) %>%
  filter(date <= trunc_date) 

## join with notification data
all_data <- x %>% 
  filter(!is.na(nhs_region)) %>%
  group_by(date, nhs_region) %>%
  summarise(count = sum(count, na.rm = T)) %>%
  ungroup %>%
  inner_join(dth_trunc,
             by = c("date","nhs_region"))

all_tot <- all_data %>%
  group_by(date) %>%
  summarise(count = sum(count, na.rm = TRUE),
            deaths = sum(deaths, na.rm = TRUE)) 

We calculate correlation with lagged NHS Pathways reports from 0 to 30 days behind deaths:


## Calculate all correlations + bootstrap CIs
lag_cor <- data.frame()
for (i in 0:30) {
  
  ## lag reports
  summary <- all_tot %>% 
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI
    getboot(.) %>%
    mutate(lag = i)

  lag_cor <- bind_rows(lag_cor, summary)
}

cor_vs_lag <- ggplot(lag_cor, aes(lag, r)) +
  theme_bw() +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi), alpha = 0.2) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_point() +
  geom_line() +
  labs(x = "Lag between NHS pathways and death data (days)",
       y = "Pearson's correlation") +
  large_txt
cor_vs_lag


l_opt <- which.max(lag_cor$r)

This analysis suggests that the best lag is 23 days. We then compare and plot the number of deaths reported against the number of NHS Pathways reports lagged by 23 days.


all_tot <- all_tot %>%
  rename(date_death = date) %>%
  mutate(note_lag = lag(count, lag_cor$lag[l_opt]),
         note_lag_c = (note_lag - mean(note_lag, na.rm = T)),
         date_note = lag(date_death,16))

lag_mod <- glm(deaths ~ note_lag, data = all_tot, family = "quasipoisson")

summary(lag_mod)
## 
## Call:
## glm(formula = deaths ~ note_lag, family = "quasipoisson", data = all_tot)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -20.902   -7.242   -3.558    4.215   14.198  
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 3.915e+00  7.107e-02   55.09   <2e-16 ***
## note_lag    2.009e-05  7.968e-07   25.21   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for quasipoisson family taken to be 50.37548)
## 
##     Null deviance: 34789  on 202  degrees of freedom
## Residual deviance: 10298  on 201  degrees of freedom
##   (23 observations deleted due to missingness)
## AIC: NA
## 
## Number of Fisher Scoring iterations: 5

exp(coefficients(lag_mod))
## (Intercept)    note_lag 
##    50.17348     1.00002
exp(confint(lag_mod))
##                 2.5 %    97.5 %
## (Intercept) 43.527260 57.517891
## note_lag     1.000019  1.000022

Rsq(lag_mod)
## [1] 0.703987

mod_fit <- as.data.frame(predict(lag_mod, type = "link", se.fit = TRUE)[1:2])

all_tot_pred <- 
  all_tot %>%
  filter(!is.na(note_lag)) %>%
  mutate(pred = mod_fit$fit,
         pred.se = mod_fit$se.fit,
         low = exp(pred - 1.96*pred.se),
         hi = exp(pred + 1.96*pred.se))


glm_fit <- all_tot_pred %>% 
    filter(!is.na(note_lag)) %>%
  ggplot(aes(x = note_lag, y = deaths)) +
  geom_point() + 
  geom_line(aes(y = exp(pred))) + 
  geom_ribbon(aes(ymin = low, ymax = hi), alpha = 0.3, col = "grey") +
  theme_bw() +
  labs(y = "Daily number of\ndeaths reported",
       x = "Daily number of NHS Pathways reports") +
  large_txt

glm_fit

4 Supplementary figures

4.1 Serial interval distribution

This is a comparison of gamma versus lognormal distribution for the serial interval used to convert r to R in our analysis. Both distributions are parameterised with mean 4.7 and standard deviation 2.9.

SI_param <- epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale, w = 0.5)

SI_distribution2 <- distcrete::distcrete("lnorm", interval = 1,
                                        meanlog = log(4.7),
                                        sdlog = log(2.9), w = 0.5)

SI_dist1 <- data.frame(x = SI_distribution$r(1e5)) 
SI_dist1 <- count(SI_dist1, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 30, 5)) +
    theme_bw()

SI_dist2 <- data.frame(x = SI_distribution2$r(1e5)) 
SI_dist2 <- count(SI_dist2, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 200, 20), limits = c(0, 200)) +
    theme_bw()


ggpubr::ggarrange(SI_dist1,
                  SI_dist2,
                  nrow = 1,
                  labels = "AUTO") 

4.2 Sensitivity analysis - 7 or 21 days moving window

We reproduce the window analysis with either a 7 or 21 days window for sensitivity purposes.

First with the 7 days window:

## set moving time window (1/2/3 weeks)
w <- 7

# create empty df
r_all_sliding_7days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_7days <- bind_rows(r_all_sliding_7days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_7days <- r_all_sliding_7days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
plot_R <- r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_7days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_7days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_7 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

Then with the 21 days window:

## set moving time window (1/2/3 weeks)
w <- 21

# create empty df
r_all_sliding_21days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_21days <- bind_rows(r_all_sliding_21days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_21days <- r_all_sliding_21days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
# plot
plot_R <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_21days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_21days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_21 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

And we combine both outputs into a single plot:


ggpubr::ggarrange(r_R_7,
                  r_R_21,
                  nrow = 2,
                  labels = "AUTO",
                  common.legend = TRUE,
                  legend = "bottom") 

4.3 Correlation between NHS Pathways reports and deaths by NHS region


lag_cor_reg <- data.frame()

for (i in 0:30) {

  summary <-
    all_data %>%
    group_by(nhs_region) %>%
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI for each region
    group_modify(~getboot(.x)) %>%
    mutate(lag = i)
  
  lag_cor_reg <- bind_rows(lag_cor_reg, summary)
}

cor_vs_lag_reg <- 
lag_cor_reg %>%
ggplot(aes(lag, r, col = nhs_region)) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi, col = NULL, fill = nhs_region), alpha = 0.2) +
  geom_point() +
  geom_line() +
  facet_wrap(~nhs_region) +
  scale_color_manual(values = pal) +
  scale_fill_manual(values = pal, guide = F) +  
  theme_bw() +
  labs(x = "Lag between NHS pathways and death data (days)", y = "Pearson's correlation", col = "NHS region") +
  theme(legend.position = "bottom") +
  guides(color = guide_legend(override.aes = list(fill = NA)))

cor_vs_lag_reg

5 Export data

We save the tables created during our analysis:


if (!dir.exists("excel_tables")) {
  dir.create("excel_tables")
}


## list all tables, and loop over export
tables_to_export <- c("r_all_sliding", "lag_cor")

for (e in tables_to_export) {
  rio::export(get(e),
              file.path("excel_tables",
                        paste0(e, ".xlsx")))
}

## also export result from regression on lagged data 
rio::export(lag_mod, file.path("excel_tables", "lag_mod.rds"))

6 System information

6.1 Outline

The following information documents the system on which the document was compiled.

6.2 System

This provides information on the operating system.

Sys.info()
##                                                                                              sysname 
##                                                                                             "Darwin" 
##                                                                                              release 
##                                                                                             "19.6.0" 
##                                                                                              version 
## "Darwin Kernel Version 19.6.0: Thu Oct 29 22:56:45 PDT 2020; root:xnu-6153.141.2.2~1/RELEASE_X86_64" 
##                                                                                             nodename 
##                                                                            "Mac-1605952442825.local" 
##                                                                                              machine 
##                                                                                             "x86_64" 
##                                                                                                login 
##                                                                                               "root" 
##                                                                                                 user 
##                                                                                             "runner" 
##                                                                                       effective_user 
##                                                                                             "runner"

6.3 R environment

This provides information on the version of R used:

R.version
##                _                           
## platform       x86_64-apple-darwin17.0     
## arch           x86_64                      
## os             darwin17.0                  
## system         x86_64, darwin17.0          
## status                                     
## major          4                           
## minor          0.3                         
## year           2020                        
## month          10                          
## day            10                          
## svn rev        79318                       
## language       R                           
## version.string R version 4.0.3 (2020-10-10)
## nickname       Bunny-Wunnies Freak Out

6.4 R packages

This provides information on the packages used:

sessionInfo()
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] ggnewscale_0.4.3     ggpubr_0.4.0         lubridate_1.7.9.2   
##  [4] chngpt_2020.10-12    cyphr_1.1.0          DT_0.16             
##  [7] kableExtra_1.3.1     janitor_2.0.1        remotes_2.2.0       
## [10] projections_0.5.1    earlyR_0.0.5         epitrix_0.2.2       
## [13] distcrete_1.0.3      incidence_1.7.3      rio_0.5.16          
## [16] reshape2_1.4.4       rvest_0.3.6          xml2_1.3.2          
## [19] linelist_0.0.40.9000 forcats_0.5.0        stringr_1.4.0       
## [22] dplyr_1.0.2          purrr_0.3.4          readr_1.4.0         
## [25] tidyr_1.1.2          tibble_3.0.4         ggplot2_3.3.2       
## [28] tidyverse_1.3.0      here_1.0.0           reportfactory_0.0.6 
## 
## loaded via a namespace (and not attached):
##  [1] minqa_1.2.4       colorspace_2.0-0  selectr_0.4-2     ggsignif_0.6.0   
##  [5] ellipsis_0.3.1    rprojroot_2.0.2   snakecase_0.11.0  fs_1.5.0         
##  [9] rstudioapi_0.13   farver_2.0.3      fansi_0.4.1       splines_4.0.3    
## [13] knitr_1.30        jsonlite_1.7.1    nloptr_1.2.2.2    broom_0.7.2      
## [17] dbplyr_2.0.0      compiler_4.0.3    httr_1.4.2        backports_1.2.0  
## [21] assertthat_0.2.1  Matrix_1.2-18     cli_2.2.0         htmltools_0.5.0  
## [25] tools_4.0.3       gtable_0.3.0      glue_1.4.2        Rcpp_1.0.5       
## [29] carData_3.0-4     cellranger_1.1.0  vctrs_0.3.5       nlme_3.1-149     
## [33] matchmaker_0.1.1  crosstalk_1.1.0.1 xfun_0.19         ps_1.4.0         
## [37] openxlsx_4.2.3    lme4_1.1-25       lifecycle_0.2.0   statmod_1.4.35   
## [41] rstatix_0.6.0     MASS_7.3-53       scales_1.1.1      hms_0.5.3        
## [45] parallel_4.0.3    sodium_1.1        yaml_2.2.1        curl_4.3         
## [49] gridExtra_2.3     stringi_1.5.3     kyotil_2020.10-12 boot_1.3-25      
## [53] zip_2.1.1         rlang_0.4.8       pkgconfig_2.0.3   evaluate_0.14    
## [57] lattice_0.20-41   labeling_0.4.2    htmlwidgets_1.5.2 cowplot_1.1.0    
## [61] tidyselect_1.1.0  plyr_1.8.6        magrittr_2.0.1    R6_2.5.0         
## [65] generics_0.1.0    DBI_1.1.0         pillar_1.4.7      haven_2.3.1      
## [69] foreign_0.8-80    withr_2.3.0       mgcv_1.8-33       survival_3.2-7   
## [73] abind_1.4-5       modelr_0.1.8      crayon_1.3.4      car_3.0-10       
## [77] utf8_1.1.4        rmarkdown_2.5     viridis_0.5.1     grid_4.0.3       
## [81] readxl_1.3.1      data.table_1.13.2 reprex_0.3.0      digest_0.6.27    
## [85] webshot_0.5.2     munsell_0.5.0     viridisLite_0.3.0